Ghost of the Heart
by Petite Moineau
Summary: An extended ending to "Ghost in the Machine". John goes on a secret mission to recover the replicator body that Elizabeth inhabited. Sheppard/Wier angst.


"Am I the only one who doesn't know how I'm supposed to feel?" McCay asked, breaking the silence at lunch table. The rest of Sheppard's team stayed silent for a few moments.

Teyla sighed at last, taking the plunge. "What do you mean?"

"I mean we thought she was dead for a while now. We already mourned her. Also I'm not entirely convinced it was actually Elizabeth." Rodney looked at his companions, searching for their opinions.

"It was her," Ronon said in his usual brusque way.

"How can you be sure?" Rodney crossed his arms over his chest.

"Ronon is right, it was Elizabeth," Teyla said. "When I spoke with her, it felt real. I told myself to doubt her, to be cautious. But only Elizabeth would have sacrificed herself like that."

"What do you think?" Rodney asked turning to Sheppard who had been uncharacteristically silent in this conversation. He usually would've told Rodney to shut up at least twice by now.

John had only been half listening. Even half-listening, he understood what they were saying. He stood up pushing his tray towards Ronon.

"I'm not hungry." He left the table.

The team watched him leave, surprised.

"I believe you have your answer, Rodney."

xXx

John activated the control console of a Jumper. He dialed the gate and took the ship through all the launch procedures before flying it through the puddle that was its namesake. He was testing out a newly repaired Jumper by flying it through a space gate and putting it through its paces both in space and in a planet's atmosphere. It was a task usually left to the other pilots on base but Woolsey had given Sheppard's team a couple days off to grieve or do whatever they needed to do to clear their heads. The return of Dr. Weir and the replicators had shaken everybody. Woolsey may have been a tight ass but even he recognized the need to look after his people's emotional and mental health. The fearless leader needed time to process what happened too, after all.

John normally would have taken advantage of the time off, catch up on some reading, watch some football, try to teach Ronon the merits of golf. He was not feeling normal though. He hadn't felt normal since Elizabeth had set foot on Atlantis again. He gave the excuse of wanting to go out and do something, giving Woolsey some spin about idle hands or whatever. Woolsey was reluctant but agreed. Who was he to say what was the best way to grieve anyway. Sheppard had other motives for this little jaunt but that didn't make his excuse entirely untrue.

Sheppard dialed a different gate so not to arouse suspicion of those stationed in the control room. Once through, he immediately dialed the gate he wanted and wasted no time going through again.

It had only been a couple days but the replicator bodies had drifted too far away to be spotted by eyes alone. He powered up the sensors and began running sweeps of the area. He only had a limited amount of time before the people back at Atlantis got worried. Luckily it didn't take long for him to locate the body that he wanted. He opened the Jumper's doors and expertly maneuvered the ship to catch the drifting body. Well the ship was certainly functional again. He closed the doors and repressurized the cabin. When it was safe for humans to breathe, he entered the cabin.

Elizabeth's body was lying prone on the floor. He picked her up and gently put her on bench. It would take some time before she was was warmed up enough to regain consciousness. He waited impatiently, pacing the length of the Jumper and occasionally checking the navigation and sensors. The HUD displayed the same information during the each five minute interval. It was during one of these regular checks that he finally heard her stirring.

"What's happening? Why I am here?" Elizabeth sat up and looked around. She locked eyes with John and her rose. "John?" Her brow furrowed in confusion and her mouth hung open disbelief.

John got up from the pilot's seat and walked over to her. Looking at the android with the likeness of Fran, he wondered how he had ever doubted her. Sheppard had so much he had planned to tell her but he forgot everything in that moment. Everything except for one thing.

"John, what's wrong?"

He pulled her into his arms, holding her tight. "I'm sorry. I'm so sorry."

After a moment she hugged him back. She broke the embrace. "It was my decision"

"No it was stupid. I was stupid. I should have trusted you." John put his hands on his hips, shaking his head. He was ashamed of how he had treated her.

"John..."

"No! When I had to leave you on the Replicator planet, that was the hardest thing I've ever had to do. I promised myself I would find you, that I would get you back. And then to find out that you were dead-" He looked down, unable to let her see, even now, how much loosing her affected him. Old habits and all that.

"You carried on. You're a survivor." She smiled a little sadly. There was a mixture of pride and loneliness in her eyes.

"I have people who depend on me, I have a job to do. I couldn't let them down." He was pacing now. "Nothing was ever the same after you...left." He definitely couldn't look at her.

Elizabeth grabbed his arm gently to still him and put her hand on the side of his face, forcing him to look at her directly. The anger and frustration melted at her touch. He looked her in the eyes. Those artificial eyes which looked back at him with such human emotions. He looked into them and saw Elizabeth staring back at him.

"I didn't even have time to get used to the fact that you were alive before you were gone again. I'm sorry I doubted you, Elizabeth." He couldn't find something to joke or shrug off. He had come here to lay everything on the table.

"You had every reason to. I can't pretend that my experience with the replicators didn't change me and in a foreign body, how could you be sure?" Elizabeth rubbed his cheek with her thumb. He was reminded of the burning kiss they had shared while host to the alien consciousnesses.

"You're still you, Elizabeth. I can see that now." John's heartbeat sped up.

"You reminded me who she was. I spent so long in company of machines, I forgot what it was to be human." Her thumb continued to stroke her face and he couldn't take it anymore.

John pulled her close to him and kissed her. These weren't the lips he remembered kissing but that surprisingly didn't bother him. Elizabeth kissed back with heat. It was much better than the first time. His head got fuzzy as her lips responded to his and her hands drifted into his hair.

He broke the kiss and smiled at her.

"Let's go home." Taking hold of her hand, he pulled her towards the cockpit but his arm was pulled tight when she wouldn't move. John looked back at her cautiously.

"Elizabeth?" His head cocked slightly to the side.

She smiled and there was an apology in her eyes, "John I can't go back."

"But I came back for you. I came back for you this time." He readjusted his grip on her hand as if saying he refused to let it go. There was a sinking feeling in his stomach like someone had dropped stone in it.

"I'm a Replicator, a threat to Atlantis." She shook her head, gently pulling her hand from his and sitting down on a bench.

"You could go ahead with your original plan: create a human body for yourself." John protested.

"I am afraid I don't know how. The others had that knowledge. If I knew how to do that I would have done it myself instead of building Replicator bodies for the others."

"But you're not a threat, Elizabeth." His hands rested defiantly on his hips.

"Maybe not intentionally, but I would be putting Atlantis at risk." She fiddled with hem of her tunic.

He knocked over the emergency gear hanging on on of the walls. The sudden movements startled Elizabeth. She closed her eyes and bowed her head.

"Damn the risks! When has that stopped us from doing what was right!" He leaned against the wall with his back to Elizabeth.

"When it protected Atlantis and the people who live there." Elizabeth raised her voice.

"I'm not abandoning you again." His voice was low with barely controlled anger.

"You don't have a choice, Colonel." Elizabeth said in her command tone.

John chuckled humorlessly, "Nice try, but you don't command me anymore."

She said nothing for the longest time and John was afraid he had said something completely wrong but he didn't turn to face her. Even if he had said something wrong the point still stood. There was no way he was going back to Atlantis alone. He couldn't do that. Not again.

"Does that mean you no longer respect my decisions?" Elizabeth asked gently.

He let out a long sigh and shoulders relaxed as he turned to face her.

"No, I just can't do what you're asking me to do." He fell to his knees in front of her burying his head in her lap. "You're asking me to kill you." His voice faltered as if the words were poison in his throat.

Tenderly, Elizabeth ran her hands through his permanently messy hair. "Elizabeth Weir is dead. I'm just a ghost. You know it's the right thing to do."

John shoulders shuddered and he looked up at her with tears in his eyes. The stone in his stomach had grown larger and heavier. He almost never cried, not from some mistaken notion of masculinity, but because he just wasn't much for crying. But this was Elizabeth. After all they had been through together, after saying goodbye too many times. To let her go again? To let her die?

"I failed you. I failed you." He couldn't stop the tears that had been welling up from flowing.

Elizabeth slipped off the seat to be eye level, kneeling on the ground with him. She took him into her arms and kissed him. John kissed her back,desperately, as if he could convince her to stay with his, as if saying what he couldn't voice.

Her hands were in his hair again and his arms wrapped around her waist. Heat pooled in his stomach as the kiss deepened, turning from desperate to passionate. When she was gone, he had held on to his memories of her. He remembered the feel of her skin when he risked himself to bring her out of the nanite-induced coma. The feel of her arounds around him when she hugged him. That special smile she seemed to reserve only for him. John kissed Elizabeth like he had always wanted to, the way he had always regretted not doing when she was gone. He poured years of sexual tension and unspoken feelings into the kiss.

Lips burning, he trailed kisses over her jawline. She tilted her head back and he moved down her neck. She moaned softly in response and pulled his face back to hers, wrapping her arms around his shoulders. Eagerly, he guided her down to the floor. His hands gripped her hips, thumbs massaging her hip bones. Elizabeth kissed his neck as well, eliciting a loud moan from his throat.

Then she stopped and sat up. Her chest rose and fell dramatically as she caught her breath. He stared at her, head still blurry, thoughts moving slowly as though through syrup.

"I'm sorry, but this isn't right." She shook her head as if still trying to convince herself.

"I love you." There it was. He hadn't planned to say it, wasn't even sure of it until the words were out. But he meant it.

"You have to go home."

"With you."

Elizabeth simply shook her head. She held him while he wept.

"I do love you, John." Her delicate hands stroked the length of his back, soothing the shuddering movements it made.

He couldn't help but think at every touch that it would be the last. Her duty to protect the people of Atlantis outweighed her desire to stay with him. And if he was honest with himself he wouldn't have felt right endangering Atlantis and his friends. But he hadn't reached that clarity yet. Right now he was trying to find the strength of will to leave the woman he loved behind once more. Eventually he pulled himself together and said the goodby he couldn't voice with one last kiss.

xXx

Back at Atlantis, Sheppard handed his report of the test flight to Woolsy. John wasn't one for lengthy reports anyway but there was a lack of flair that he usually liked to put in his reports. This, no doubt, is what prompted the new commander to inquire after Sheppard's well-being. The Colonel shrugged it off and left. He could tell Woolsy suspected something was wrong but he didn't press the matter. The new commander was at last learning some tact.

On the way back to his apartment, John ran into Teyla and Ronon. They exchanged small talk, avoiding the subject they didn't want to think about much less talk about. But something in his friends eyes told him they knew what he had done. Their silence communicated their support and empathy.

John bid them goodnight and went home, his mind full of Elizabeth. He knew this would hang over him the rest of his life. Though he couldn't have brought her back, he still felt guilt for leaving her behind, for letting her die. Eventually he might stop hating himself, but that was far off. Till then he would focus on his missions and the protection of Atlantis and of Earth. It's what she would have wanted.

~The End

**A/N: I always felt Elizabeth's goodbye was not as emotional as it should have been and this is kinda what I imagine John doing. Obviously whether or not you believe John and Elizabeth had feelings for each other, I still feel like he would have made the effort to rescue her. He's always been the "leave no one behind" kind of person. Anyway, I hope you all liked it and thank you so much for reading!**


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